[English] 日本語
Yorodumi
- PDB-9bqw: Fab F945-DbpA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bqw
TitleFab F945-DbpA complex
Components
  • Decorin-binding protein A
  • F945 Fab Heavy Chain
  • F945 Fab Light Chain
KeywordsIMMUNE SYSTEM / Fragment antigen binding Fab / Decorin binding protein.
Function / homology: / Decorin-binding protein / Decorin-binding superfamily / Decorin binding protein / membrane / Decorin-binding protein A
Function and homology information
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsRudolph, M.J. / Mantis, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00040 United States
CitationJournal: Front Immunol / Year: 2025
Title: Germline encoded residues dominate the interaction of a human monoclonal antibody with decorin binding protein A of Borrelia burgdorferi.
Authors: Rudolph, M.J. / Muriuki, B.M. / Chen, Y. / Vance, D.J. / Vorauer, C. / Piazza, C.L. / Freeman-Gallant, G. / Golonka, R.M. / Mirabile, G. / Guttman, M. / Cavacini, L.A. / Mantis, N.J.
History
DepositionMay 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Decorin-binding protein A
H: F945 Fab Heavy Chain
L: F945 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,36710
Polymers65,6953
Non-polymers6727
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.105, 86.461, 151.484
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein Decorin-binding protein A


Mass: 18039.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Strain: B31 / Gene: dbpA, BB_A24 / Production host: Escherichia coli (E. coli) / References: UniProt: O50917
#2: Antibody F945 Fab Heavy Chain


Mass: 24283.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody F945 Fab Light Chain


Mass: 23371.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: PEG 3350 and 200 mM Ammonium Sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 22519 / % possible obs: 99.3 % / Redundancy: 11.1 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.038 / Rrim(I) all: 0.13 / Χ2: 0.381 / Net I/σ(I): 3.3 / Num. measured all: 249397
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.55-2.595.90.7969940.80.9430.3020.8560.1990.7
2.59-2.646.60.73210780.8260.9510.2660.7830.18897.3
2.64-2.697.70.72811250.8460.9570.2520.7740.19998.7
2.69-2.7590.6710720.9180.9780.2210.7070.20899.6
2.75-2.81100.6111340.9260.9810.1920.6410.21599.9
2.81-2.8710.80.54411140.9460.9860.1660.5690.22799.7
2.87-2.9411.50.45911010.9640.9910.1370.480.22699.9
2.94-3.0211.90.38211340.9740.9940.1130.3990.245100
3.02-3.1112.10.34111060.9820.9950.1010.3560.264100
3.11-3.2111.60.27211360.9870.9970.0830.2850.289100
3.21-3.3311.70.22411000.990.9980.0680.2350.303100
3.33-3.4612.10.19611400.9920.9980.0590.2050.35899.9
3.46-3.6212.40.15611240.9930.9980.0470.1630.40499.9
3.62-3.8113.20.13311250.9950.9990.0390.1380.436100
3.81-4.0513.10.10911370.9970.9990.0310.1130.47899.9
4.05-4.3612.70.0911440.9970.9990.0260.0940.549100
4.36-4.812.70.07711490.9960.9990.0230.080.597100
4.8-5.4912.30.07411570.9980.9990.0220.0770.538100
5.49-6.9211.10.07611740.9970.9990.0240.080.556100
6.92-5011.90.06512750.9980.9990.020.0680.658100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→48.42 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 1087 4.84 %
Rwork0.2024 --
obs0.2045 22454 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4284 0 35 57 4376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034419
X-RAY DIFFRACTIONf_angle_d0.6045996
X-RAY DIFFRACTIONf_dihedral_angle_d4.791604
X-RAY DIFFRACTIONf_chiral_restr0.043677
X-RAY DIFFRACTIONf_plane_restr0.005766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.660.41511150.34872478X-RAY DIFFRACTION93
2.66-2.810.29461360.26942639X-RAY DIFFRACTION99
2.81-2.980.32121320.24372663X-RAY DIFFRACTION100
2.98-3.210.34921430.25422653X-RAY DIFFRACTION100
3.21-3.530.2641330.22212651X-RAY DIFFRACTION100
3.53-4.050.21931360.18112705X-RAY DIFFRACTION100
4.05-5.10.18461440.15232721X-RAY DIFFRACTION100
5.1-48.420.22311480.18962857X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.4818-1.2899-0.2964.84133.38482.45780.0315-0.26270.43340.60660.3430.08950.61560.6653-0.6310.2996-0.0020.03950.4533-0.0150.3879-26.759247.1321-26.4977
23.9487-0.50563.28143.47340.06473.3301-0.53580.08280.48250.3016-0.1564-0.0986-1.0870.4848-0.14490.2864-0.08730.07850.39920.03830.4408-34.004754.1124-24.7965
32.79830.51452.5841.94561.6686.0951-0.2122-0.11970.37670.14260.02180.178-0.457-0.11750.26130.33480.0420.05460.41050.01120.4391-41.761750.1063-24.607
41.4364-0.8704-0.02546.343-1.81521.62030.03190.205-0.3033-0.5605-0.1504-0.27230.75960.54630.11570.51560.17760.04170.4341-0.0250.3802-40.107720.9552-30.3141
55.2735-0.5196-2.12764.21260.65242.6303-0.07820.7473-0.2776-0.7855-0.03710.47330.4989-0.34380.11050.87020.0491-0.14470.4687-0.09420.5552-58.3698-3.2886-25.7341
69.49813.19660.55195.1839-0.32711.1508-0.18650.04220.0088-0.0520.1093-0.42250.50930.22710.1650.490.1022-0.03240.3802-0.00180.2702-47.661424.5187-5.0814
73.38421.7985-2.11995.5181-1.7633.86940.0201-0.1335-0.10070.0601-0.08090.01360.20620.14730.02020.24940.0687-0.00430.3178-0.03380.2255-51.041626.3895-12.2666
83.3017-1.869-0.91196.71591.09321.3439-0.27660.1718-0.85940.2713-0.13950.54510.6716-0.03630.4140.8445-0.07460.04450.4075-0.02980.6644-58.9299-10.0034-10.5014
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 108 )
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 176 )
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 119 )
5X-RAY DIFFRACTION5chain 'H' and (resid 120 through 222 )
6X-RAY DIFFRACTION6chain 'L' and (resid 1 through 25 )
7X-RAY DIFFRACTION7chain 'L' and (resid 26 through 112 )
8X-RAY DIFFRACTION8chain 'L' and (resid 113 through 212 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more